I recently asked about help finding promoters in particular, and got a helpful pointer for that... however, it wasn't exactly what I wanted I found out.
I then found something much closer to what I wanted: the Integrated Genome Viewer has a "Motif Finder" tool, and you can even enter in ambiguous nucleotides to it. The only catch (for me at least) is... is there a command line tool like it? Do I have to interact with IGV through the GUI? It seems there is some command line support for IGV, but it seems like it is geared more for pre-processing. Sorry if I missed something though, would appreciate any pointers!